Red Blood Cell and Platelet Phenotype Prediction from Whole Genome Sequencing in 621 Sickle Cell Disease Patients: Correlation with Alloimmunization History, Serology and Other Genotyping Methods

• Published in: Blood 2018-11, Vol.132 (Supplement 1), p.2388-2388
• Main Authors: Montemayor Garcia, Celina, Weisman, Julie K., Gandla, Divya, Long, James Owen, Dalgard, Clifton Lee, Pirooznia, Mehdi, Klein, Harvey, Thein, Swee Lay
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2018-99-115008

Introduction: Red blood cell (RBC) transfusions are central in the management of sickle cell disease (SCD), an inherited hemoglobinopathy characterized by hemolysis, acute pain, and multi-systemic complications. Extended matching of patient and donor RBC antigens is an established strategy to minimize alloimmunization, which can make provision of compatible blood difficult and can result in severe, even lethal hemolytic transfusion reactions. While RBC genotype matching has proven valuable in SCD transfusion practice, current technologies are often limited in throughput and focus on selected blood groups and known variants. Limited information is available comparing whole genome sequencing (WGS) with other blood typing platforms in SCD. Design/Methods: WGS was performed on stored blood samples from 621 SCD patients recruited into two clinical studies. We utilized our open-source Python application (RyLAN), to translate WGS data into a predicted extended RBC and platelet phenotype. The 467 genomic variants interpreted by RyLAN in 41 genes were correlated with clinical and laboratory data in the immunohematology and electronic health records (Figure 1). Results: The 621 patients included 485 HbSS, 21 HbSb0, 29 HbSβ+, 84 HbSC, 1HbS O Arab, and 1 HbSD. The mean age was 34.3 ± 12.1 years, and 54% were female. Health records indicated that 383 (62%) patients had previously received RBC transfusions and 17(3%) had never been transfused; the status of the remaining 221 was unknown. RyLAN software was executed as a singularity container in multithreaded mode, completing the analysis of all 621 bam WGS files in 8.5 hours (8 CPUs and 16GB of memory per file). The average read depth for genomic positions of interest was 33 and the average QUAL value was 644. The highest variant allele frequency was detected at the Fyb, ACKR1 promoter, and the KCAM- loci (94%, 86% and 82%, respectively). Each of the 621 participants demonstrated a unique extended blood group genotype through WGS. RyLAN predicted 237 unique extended platelet phenotype combinations in this cohort, including HPA-25bw and HPA-13bw positive patients. Blood antigen WGS predictions were correlated with other typing methods in 112 individuals: 192 total serologic reactions for 8 antigens; 55 documented alloantibodies; 25 genomic variants in 71 participants by probe-elongation array; and PCR with sequence-specific primers for 8 variants in 13 individuals (Figure 1). Two instances of heterozygosity (Jka/Jkb and